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Ubuntu 14.04 has a modern gcc compared with Centos 6 which requires b…
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…oost::shared_ptr to be used explictly.

This had regressed when triphic_subs.cc was updated to include tautomers, those changes being written on a
Centos 6 machine.
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@DavidACosgrove
DavidACosgrove committed Feb 22, 2016
1 parent 18a7dc3 commit 7db4bbe
Showing 1 changed file with 64 additions and 64 deletions.
128 changes: 64 additions & 64 deletions src/triphic_subs.cc
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Expand Up @@ -46,7 +46,7 @@ using namespace OEChem;
using namespace OESz;
using namespace OEConfGen;

typedef shared_ptr<OEMol> pOEMol;
typedef boost::shared_ptr<OEMol> pOEMol;

namespace DACLIB {
void read_smarts_file( const string &smarts_file ,
Expand Down Expand Up @@ -81,8 +81,8 @@ void score_and_store_cliques( const string &query_name , int query_conf_num ,
vector<SinglePPhoreSite *> &query_score_sites ,
vector<SinglePPhoreSite *> &target_sites ,
OEMol *target_mol , int target_conf_num ,
shared_ptr<DACLIB::VolumeGrid> &query_solid_grid ,
shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &query_solid_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
const vector<pair<string,DACLIB::VolumeGrid *> > &score_vol_grids ,
const vector<vector<int> > &cliques ,
GtplDefs::DIRS_USAGE ring_norm_usage ,
Expand All @@ -103,7 +103,7 @@ void score_and_store_cliques( const string &query_name , int query_conf_num ,
const vector<string> &required_sites_and ,
const vector<string> &required_points_or ,
const vector<string> &required_points_and ,
shared_ptr<OESzybki> &szybki ,
boost::shared_ptr<OESzybki> &szybki ,
list<OverlayScore *> &clique_overlays );
// this also in score_and_store_cliques.cc
bool add_overlay_score_to_list( OverlayScore *new_score ,
Expand All @@ -116,7 +116,7 @@ void overlay_mols_and_sites( OEMol *target_mol ,
bool use_h_vectors , bool use_lps ,
OEMolBase *&target_conf );
// and this
float optimise_overlay( shared_ptr<OESzybki> &szybki ,
float optimise_overlay( boost::shared_ptr<OESzybki> &szybki ,
OEMolBase *target_conf ,
vector<SinglePPhoreSite *> &ov_target_sites );

Expand Down Expand Up @@ -314,15 +314,15 @@ void read_query_file( TriphicSettings &ts ,

// ********************************************************************
void read_protein_file( const string &protein_file ,
shared_ptr<OEMolBase> &protein ) {
boost::shared_ptr<OEMolBase> &protein ) {

if( protein_file.empty() )
return;

oemolistream ims( protein_file.c_str() );
if( !ims )
throw DACLIB::FileReadOpenError( protein_file.c_str() );
protein = shared_ptr<OEMolBase>( OENewMolBase( OEMolBaseType::OEDefault ) );
protein = boost::shared_ptr<OEMolBase>( OENewMolBase( OEMolBaseType::OEDefault ) );
ims >> *protein;

}
Expand Down Expand Up @@ -355,35 +355,35 @@ void read_subset_file( const string &subset_file ,

// ********************************************************************
void prepare_query_volume_grids( OEMolBase *query_mol ,
shared_ptr<DACLIB::VolumeGrid> &query_grid ,
shared_ptr<OEMolBase> &protein ,
shared_ptr<DACLIB::VolumeGrid> &protein_grid ) {
boost::shared_ptr<DACLIB::VolumeGrid> &query_grid ,
boost::shared_ptr<OEMolBase> &protein ,
boost::shared_ptr<DACLIB::VolumeGrid> &protein_grid ) {

// prepare_mol_grid puts surface and core markers into the grid, so can
// do single conf against single conf volume and surface volume calcs in
// one go. Even if we're not sorting or filtering using GRID_SHAPE_TANI,
// we'll want to calculate the final number of the grid_shape_tani,
// included and total vols.
if( query_mol && *query_mol ) {
query_grid = shared_ptr<DACLIB::VolumeGrid>( DACLIB::prepare_mol_grid( query_mol ) );
query_grid = boost::shared_ptr<DACLIB::VolumeGrid>( DACLIB::prepare_mol_grid( query_mol ) );
} else {
query_grid = shared_ptr<DACLIB::VolumeGrid>( static_cast<DACLIB::VolumeGrid *>( 0 ) );
query_grid = boost::shared_ptr<DACLIB::VolumeGrid>( static_cast<DACLIB::VolumeGrid *>( 0 ) );
}

if( !protein ) {
return; // no protein
}

protein_grid = shared_ptr<DACLIB::VolumeGrid>( DACLIB::prepare_mol_grid( protein.get() ) );
protein_grid = boost::shared_ptr<DACLIB::VolumeGrid>( DACLIB::prepare_mol_grid( protein.get() ) );

}

// ********************************************************************
void prepare_szybki_optimiser( const TriphicSettings &ts ,
shared_ptr<OEMolBase> &protein ,
shared_ptr<OESzybki> &szybki ) {
boost::shared_ptr<OEMolBase> &protein ,
boost::shared_ptr<OESzybki> &szybki ) {

szybki = shared_ptr<OESzybki>( new OESzybki );
szybki = boost::shared_ptr<OESzybki>( new OESzybki );
szybki->SetProtein( *protein ); // rigid by default
szybki->SetProteinElectrostaticModel( OEProteinElectrostatics::NoElectrostatics );

Expand Down Expand Up @@ -413,8 +413,8 @@ void overlay_hit_and_store( OEMol &target_mol ,
vector<BasePPhoreSite *> &query_sites ,
vector<SinglePPhoreSite *> &query_score_sites ,
vector<vector<SinglePPhoreSite *> > &target_sites ,
shared_ptr<DACLIB::VolumeGrid> &query_grid ,
shared_ptr<DACLIB::VolumeGrid> protein_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &query_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> protein_grid ,
const vector<pair<string,DACLIB::VolumeGrid *> > &score_vol_grids ,
bool use_ring_norms , bool use_h_vectors ,
bool use_lps ,
Expand Down Expand Up @@ -617,10 +617,10 @@ void output_results( OEMolBase *query_mol ,
}

// ********************************************************************
bool not_smarts_hit( vector<shared_ptr<OESubSearch> > &not_smarts_subs ,
bool not_smarts_hit( vector<boost::shared_ptr<OESubSearch> > &not_smarts_subs ,
OEMol &target_mol ) {

vector<shared_ptr<OESubSearch> >::iterator p , ps;
vector<boost::shared_ptr<OESubSearch> >::iterator p , ps;
for( p = not_smarts_subs.begin() , ps = not_smarts_subs.end() ;
p != ps ; ++p ) {
if( (*p)->SingleMatch( target_mol ) )
Expand All @@ -637,8 +637,8 @@ void store_hits( list<OverlayScore *> &this_query_hits ,
vector<BasePPhoreSite *> &query_sites ,
vector<SinglePPhoreSite *> &query_score_sites ,
vector<vector<SinglePPhoreSite *> > &target_sites ,
shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
const vector<pair<string,DACLIB::VolumeGrid *> > &score_vol_grids ,
OEMolBase *query_mol , OEMol &target_mol ,
TriphicSettings &ts ,
Expand Down Expand Up @@ -756,11 +756,11 @@ void search_target_molecule( vector<pair<string,string> > &input_smarts ,
vector<BasePPhoreSite *> &query_sites ,
vector<SinglePPhoreSite *> &query_score_sites ,
TriphicSettings &ts ,
shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
const vector<pair<string,DACLIB::VolumeGrid *> > &score_vol_grids ,
shared_ptr<OESzybki> &szybki ,
vector<shared_ptr<OESubSearch> > &not_smarts_subs ,
boost::shared_ptr<OESzybki> &szybki ,
vector<boost::shared_ptr<OESubSearch> > &not_smarts_subs ,
OEMol &target_mol ,
list<OverlayScore *> &hit_list ) {

Expand Down Expand Up @@ -994,7 +994,7 @@ void send_results_to_master( list<OverlayScore *> &hits ) {

// ********************************************************************
void do_omega_if_necessary( vector<pOEMol> &prepped_target_mols ,
shared_ptr<OEOmega> &omega ,
boost::shared_ptr<OEOmega> &omega ,
bool do_omega , bool do_flipper ,
bool do_warts ,
unsigned int max_versions ,
Expand Down Expand Up @@ -1037,7 +1037,7 @@ void do_omega_if_necessary( vector<pOEMol> &prepped_target_mols ,
if( do_omega || ( prepped_target_mols[i]->NumAtoms() &&
3 != prepped_target_mols[i]->GetDimension() ) ) {
if( !omega && OEOmegaIsLicensed( "toolkit" ) ) {
omega = shared_ptr<OEOmega>( new OEOmega );
omega = boost::shared_ptr<OEOmega>( new OEOmega );
}
(*omega)( *(out_mols[i]) );
OESetDimensionFromCoords( *out_mols[i] );
Expand Down Expand Up @@ -1074,7 +1074,7 @@ void do_omega_if_necessary( vector<pOEMol> &prepped_target_mols ,
}

// ********************************************************************
void prepare_search_molecule( OEMol &target_mol , shared_ptr<OEOmega> &omega ,
void prepare_search_molecule( OEMol &target_mol , boost::shared_ptr<OEOmega> &omega ,
bool do_omega , bool do_flipper ,
bool do_ions_and_tauts , bool do_warts ,
unsigned int max_versions ,
Expand All @@ -1084,7 +1084,7 @@ void prepare_search_molecule( OEMol &target_mol , shared_ptr<OEOmega> &omega ,
// Suppress irritating warnings from OELibraryGen (and everything else, of course, but
// OELibraryGen gives a lot of very irritating stuff)
OESystem::OEThrow.SetLevel( OESystem::OEErrorLevel::Error );
shared_ptr<OEMolBase> sc_target_mol( OENewMolBase( target_mol.SCMol() ,
boost::shared_ptr<OEMolBase> sc_target_mol( OENewMolBase( target_mol.SCMol() ,
OEMolBaseType::OEDefault ) );
vector<OEMolBase *> tm = enumerate_tautomers( *sc_target_mol , string( "" ) ,
string( "" ) );
Expand Down Expand Up @@ -1183,11 +1183,11 @@ void search_database( unsigned int next_mol , int step_size ,
vector<SinglePPhoreSite *> &query_score_sites ,
const vector<string> &mol_subset ,
TriphicSettings &ts ,
shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
const vector<pair<string,DACLIB::VolumeGrid *> > &score_vol_grids ,
shared_ptr<OESzybki> &szybki , shared_ptr<OEOmega> &omega ,
vector<shared_ptr<OESubSearch> > &not_smarts_subs ,
boost::shared_ptr<OESzybki> &szybki , boost::shared_ptr<OEOmega> &omega ,
vector<boost::shared_ptr<OESubSearch> > &not_smarts_subs ,
list<OverlayScore *> &hit_list ) {

for( int i = 0 ; i < step_size ; ++i ) {
Expand Down Expand Up @@ -1243,7 +1243,7 @@ void search_database( unsigned int next_mol , int step_size ,
// ********************************************************************
void make_not_smarts_queries( const vector<pair<string,string> > &not_smarts_list ,
vector<pair<string,string> > &smarts_sub_defn ,
vector<shared_ptr<OESubSearch> > &not_smarts_subs ) {
vector<boost::shared_ptr<OESubSearch> > &not_smarts_subs ) {

for( int i = 0 , is = not_smarts_list.size() ; i < is ; ++i ) {
string exp_smarts( not_smarts_list[i].second );
Expand All @@ -1259,7 +1259,7 @@ void make_not_smarts_queries( const vector<pair<string,string> > &not_smarts_lis
<< "in make_not_smarts_queries()" << endl;
throw( DACLIB::SMARTSDefnError( oss.str().c_str() ) );
}
not_smarts_subs.push_back( shared_ptr<OESubSearch>( new OESubSearch( exp_smarts.c_str() ) ) );
not_smarts_subs.push_back( boost::shared_ptr<OESubSearch>( new OESubSearch( exp_smarts.c_str() ) ) );
}

}
Expand All @@ -1269,8 +1269,8 @@ void make_not_smarts_queries( const vector<pair<string,string> > &not_smarts_lis
// which will be used in the Pareto rankings.
OverlayScore *make_reference_overlay( OEMolBase *query_mol ,
vector<BasePPhoreSite *> &query_sites ,
shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
vector<pair<string,DACLIB::VolumeGrid *> > &score_vol_grids ) {

vector<int> clique = vector<int>( 2 * query_sites.size() , 0 );
Expand All @@ -1282,7 +1282,7 @@ OverlayScore *make_reference_overlay( OEMolBase *query_mol ,
}

OEMol query_cp( *query_mol );
shared_ptr<OESz::OESzybki> szybki( static_cast<OESz::OESzybki *>( 0 ) );
boost::shared_ptr<OESz::OESzybki> szybki( static_cast<OESz::OESzybki *>( 0 ) );
try {
OverlayScore *ret_val = new OverlayScore( string( query_mol->GetTitle() ) , string( query_mol->GetTitle() ) ,
0 , 0 , clique , query_sites ,
Expand Down Expand Up @@ -1314,14 +1314,14 @@ void setup_search( TriphicSettings &ts ,
OEMolBase *&query_mol ,
vector<BasePPhoreSite *> &query_sites ,
vector<SinglePPhoreSite *> &query_score_sites ,
shared_ptr<OEMolBase> &protein ,
boost::shared_ptr<OEMolBase> &protein ,
vector<string> &mol_subset ,
shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &query_vol_grid ,
boost::shared_ptr<DACLIB::VolumeGrid> &protein_grid ,
vector<pair<string,DACLIB::VolumeGrid *> > &score_vol_grids ,
shared_ptr<OESzybki> &szybki ,
shared_ptr<OEOmega> &omega ,
vector<shared_ptr<OESubSearch> > &not_smarts_subs ,
boost::shared_ptr<OESzybki> &szybki ,
boost::shared_ptr<OEOmega> &omega ,
vector<boost::shared_ptr<OESubSearch> > &not_smarts_subs ,
bool report_sites ) {

if( !ts.smarts_file().empty() && !ts.points_file().empty() ) {
Expand Down Expand Up @@ -1398,7 +1398,7 @@ void setup_search( TriphicSettings &ts ,
}

if( ts.do_omega() ) {
omega = shared_ptr<OEOmega>( new OEOmega );
omega = boost::shared_ptr<OEOmega>( new OEOmega );
}

// SMARTS that the hits can't match
Expand Down Expand Up @@ -1484,14 +1484,14 @@ int serial_triphic_search( TriphicSettings &ts ) {
OEMolBase *query_mol;
vector<BasePPhoreSite *> query_sites;
vector<SinglePPhoreSite *> query_score_sites;
shared_ptr<OEMolBase> protein;
boost::shared_ptr<OEMolBase> protein;
vector<string> mol_subset;
shared_ptr<DACLIB::VolumeGrid> query_vol_grid;
shared_ptr<DACLIB::VolumeGrid> protein_grid;
boost::shared_ptr<DACLIB::VolumeGrid> query_vol_grid;
boost::shared_ptr<DACLIB::VolumeGrid> protein_grid;
vector<pair<string,DACLIB::VolumeGrid *> > score_vol_grids;
shared_ptr<OESzybki> szybki;
shared_ptr<OEOmega> omega;
vector<shared_ptr<OESubSearch> > not_smarts_subs;
boost::shared_ptr<OESzybki> szybki;
boost::shared_ptr<OEOmega> omega;
vector<boost::shared_ptr<OESubSearch> > not_smarts_subs;
oemolistream *ims = 0;

setup_search( ts , input_smarts , smarts_sub_defn , pharm_points ,
Expand Down Expand Up @@ -1730,14 +1730,14 @@ void parallel_triphic_search( TriphicSettings &ts , int world_size ) {
OEMolBase *query_mol;
vector<BasePPhoreSite *> query_sites;
vector<SinglePPhoreSite *> query_score_sites;
shared_ptr<OEMolBase> protein;
boost::shared_ptr<OEMolBase> protein;
vector<string> mol_subset;
shared_ptr<DACLIB::VolumeGrid> query_vol_grid;
shared_ptr<DACLIB::VolumeGrid> protein_grid;
boost::shared_ptr<DACLIB::VolumeGrid> query_vol_grid;
boost::shared_ptr<DACLIB::VolumeGrid> protein_grid;
vector<pair<string,DACLIB::VolumeGrid *> > score_vol_grids;
shared_ptr<OESzybki> szybki;
shared_ptr<OEOmega> omega;
vector<shared_ptr<OESubSearch> > not_smarts_subs;
boost::shared_ptr<OESzybki> szybki;
boost::shared_ptr<OEOmega> omega;
vector<boost::shared_ptr<OESubSearch> > not_smarts_subs;
setup_search( ts , input_smarts , smarts_sub_defn , pharm_points ,
query_mol , query_sites , query_score_sites , protein ,
mol_subset , query_vol_grid , protein_grid ,
Expand Down Expand Up @@ -1789,14 +1789,14 @@ void slave_event_loop() {
OEMolBase *query_mol;
vector<BasePPhoreSite *> query_sites;
vector<SinglePPhoreSite *> query_score_sites;
shared_ptr<OEMolBase> protein;
boost::shared_ptr<OEMolBase> protein;
TriphicSettings ts;
vector<string> mol_subset;
shared_ptr<DACLIB::VolumeGrid> query_vol_grid;
shared_ptr<DACLIB::VolumeGrid> protein_grid;
shared_ptr<OESzybki> szybki;
shared_ptr<OEOmega> omega;
vector<shared_ptr<OESubSearch> > not_smarts_subs;
boost::shared_ptr<DACLIB::VolumeGrid> query_vol_grid;
boost::shared_ptr<DACLIB::VolumeGrid> protein_grid;
boost::shared_ptr<OESzybki> szybki;
boost::shared_ptr<OEOmega> omega;
vector<boost::shared_ptr<OESubSearch> > not_smarts_subs;
list<OverlayScore *> hit_list;
vector<pair<string,DACLIB::VolumeGrid *> > score_vol_grids;

Expand Down

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